# Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

## Documentation for package ‘scp’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aggregateFeaturesOverAssays | Aggregate features over multiple assays
computeMedianCV_SCoPE2 | (Deprecated) Compute the median coefficient of variation (CV) per cell
computeSCR | Compute the sample over carrier ratio (SCR)
divideByReference | Divide assay columns by a reference column
medianCVperCell | Compute the median coefficient of variation (CV) per cell
mqScpData | Example MaxQuant/SCoPE2 output
normalizeSCP | Normalize single-cell proteomics (SCP) data
pep2qvalue | Compute q-values
readSCP | Read single-cell proteomics data as a QFeatures object from tabular data and metadata
readSingleCellExperiment | Read SingleCellExperiment from tabular data
rowDataToDF | Extract the 'rowData' of a 'QFeatures' object to a 'DataFrame'
sampleAnnotation | Single cell sample annotation
scp1 | Single Cell QFeatures data